8TQ0

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with (R)-Lipoic Acid

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8087567	3000260	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00850	e8tq0A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)
B	PF00850	e8tq0B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: PF00850	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hdac6 protein	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transition metal ion binding zinc ion binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transition metal ion binding zinc ion binding tubulin deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity histone modifying activity	regulation of biological process organonitrogen compound metabolic process regulation of protein modification process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule deacylation protein deacetylation regulation of primary metabolic process regulation of tubulin deacetylation protein deacylation organic substance metabolic process regulation of protein deacetylation tubulin deacetylation regulation of biological process organonitrogen compound metabolic process regulation of protein modification process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule deacylation protein deacetylation regulation of primary metabolic process regulation of tubulin deacetylation protein deacylation organic substance metabolic process regulation of protein deacetylation tubulin deacetylation macromolecule modification metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of metabolic process developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development definitive hemopoiesis cellular developmental process hemopoiesis cell differentiation cell development cellular process behavior locomotory behavior swimming behavior hematopoietic progenitor cell differentiation regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000286	Histone deacetylase family	Family
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR023801	Histone deacetylase domain	Domain
A, B	IPR001607	Zinc finger, UBP-type	Domain
A, B	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A, B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.